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Crystal Structure of H60N/Y130F double mutant of ChmJ, a 3'-monoepimerase from Streptomyces bikiniensis in complex with dTDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HMZ PDB entry 4HMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 20% PEG 3400, 2% 3-methyl-1,5-pentanediol, 100 mM MOPS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.24 62.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.017 α = 90 b = 141.017 β = 90 c = 116.434 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210r 2012-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.979 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.6 99.71 96.1 4.9 143838 143838
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 93.6 0.39 2.07 2.8 13940
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4HMZ 1.6 30 136644 7194 96.07 0.21385 0.21173 0.2123 0.25373 0.2534 RANDOM 29.798
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.27 0.27 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.968 r_dihedral_angle_4_deg 17.972 r_dihedral_angle_3_deg 15.766 r_scangle_it 7.556 r_dihedral_angle_1_deg 6.28 r_scbond_it 4.891 r_mcangle_it 3.194 r_angle_refined_deg 2.313 r_mcbond_it 2.046 r_chiral_restr 0.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.968 r_dihedral_angle_4_deg 17.972 r_dihedral_angle_3_deg 15.766 r_scangle_it 7.556 r_dihedral_angle_1_deg 6.28 r_scbond_it 4.891 r_mcangle_it 3.194 r_angle_refined_deg 2.313 r_mcbond_it 2.046 r_chiral_restr 0.178 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6250 Nucleic Acid Atoms Solvent Atoms 419 Heterogen Atoms 196
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling